PLUMED-NEST

Project ID: plumID:19.060
Source: 2_ala2/simulation/plumed.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

# Load file
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=../../0_code/NeuralNetworkVes.cpp

# set up two variables for Phi and Psi dihedral angles 
phi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5,7,9,15
The TORSION action with label phi calculates a scalar quantitypsi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17

# nn bias
The TORSION action with label psi calculates a scalar quantity
NN_VES
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
LABEL=nn
ARG=phi 
NODES=48,24,12 
OPTIM=ADAM
ACTIVATION=RELU
GRID_MIN=-pi 
GRID_MAX=pi 
GRID_BIN=50 
TEMP=300
AVE_STRIDE=500
PRINT_STRIDE=1000 
TARGET_STRIDE=1 
GAMMA=10
LRATE=0.001 
TAU_KL=10000
DECAY=1000
ADAPTIVE_DECAY=0.5
... NN_VES

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
ARG
the input for this action is the scalar output from one or more other actions
 
FILE
the name of the file on which to output these quantities
=COLVAR 
FMT
the format that should be used to output real numbers
=%10.8f